\HeaderA{printorder}{Identify Order in which Spots were Printed}{printorder}
\keyword{IO}{printorder}
\begin{Description}\relax
Identify order in which spots were printed and the 384-well plate from which they were printed.
\end{Description}
\begin{Usage}
\begin{verbatim}
printorder(layout, ndups=1, spacing="columns", npins, start="topleft")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{layout}] list with the components \code{ngrid.r}, \code{ngrid.c}, \code{nspot.r} and \code{nspot.c}, or an \code{RGList} or \code{MAList} object from which the printer layout may be extracted.
\item[\code{ndups}] number of duplicate spots, i.e., number of times print-head dips into each well
\item[\code{spacing}] character string indicating layout of duplicate spots.
Choices are \code{"columns"}, \code{"rows"} or \code{"topbottom"}.
\item[\code{npins}] actual number of pins or tips on the print-head
\item[\code{start}] character string giving position of the spot printed first in each grid.
Choices are \code{"topleft"} or \code{"topright"} and partial matches are accepted.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
In most cases the printer-head contains the \code{layout\$ngrid.r} times \code{layout\$ngrid.c} pins or tips and the array is printed using \code{layout\$nspot.r} times \code{layout\$npot.c} dips of the head.
The plate holding the DNA to be printed is assumed to have 384 wells in 16 rows and 24 columns.

\code{ndups} indicates the number of spots printed from each well.
The replicate spots from multiple dips into the same wells are assumed to be side-by-side by columns (\code{spacing="columns"}), by rows (\code{spacing="rows"}) or in the top and bottom halves of the array (\code{spacing="topbottom"}).

In some cases a smaller number of physical pins is used and the total number of grids is built up by effectively printing two or more sub-arrays on the same slide.
In this case the number of grids should be a multiple of the number of pins.

Printing is assumed to proceed by rows within in each grid starting either from the top-left or the top-right.
\end{Details}
\begin{Value}
List with components
\begin{ldescription}
\item[\code{printorder}] numeric vector giving printorder of each spot, i.e., which dip of the print-head was used to print it
\item[\code{plate}] numeric vector giving plate number from which each spot was printed
\item[\code{plate.r}] numeric vector giving plate-row number of the well from which each spot was printed
\item[\code{plate.c}] numeric vector giving plate-column number of the well from which each spot was printed
\item[\code{plateposition}] character vector summarizing plate number and plate position of the well from which each spot was printed with letters for plate rows and number for columns.
For example \code{02B13} is second row, 13th column, of the second plate.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{normalizeForPrintorder}{normalizeForPrintorder}}.

An overview of LIMMA functions for reading data is given in \LinkA{03.ReadingData}{03.ReadingData}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
printorder(list(ngrid.r=2,ngrid.c=2,nspot.r=12,nspot.c=8))
\end{ExampleCode}
\end{Examples}